Phantom
by Nate Grey
Summary: The soul inside of Unit 00 definitely hates Rei, but not for the reasons you might think.


Disclaimer: Neon Genesis Evangelion belongs to GAINAX, and I make no profit from this.

Warning: I wrote this largely in defense of my beliefs concerning the erratic behavior of Unit 00. If you're convinced that Unit 00 houses Naoko Akagi's soul, you won't agree with any of this. All I ask is that if you start the story, finish it before you cast judgment (or any sort of rotten foods) at me.

Summary: Inside Unit 00 lurks a shadow from Rei Ayanami's past, but even shadows can reach into the light.

**Phantom**

**A Neon Genesis Evangelion Oneshot**

**by Nate Grey (XMAN0123-at-aol-dot-com)**

* * *

It was always very curious to her, how differently people reacted to the same things.

Take a synchronization test, for example.

Dr. Akagi approached them as she did nearly everything: with cool, clinical precision and unfailing confidence in her own abilities.

Major Katsuragi was nearly the exact opposite. Every synch test seemed to invoke a healthy dose of nervousness in her, as if she were the one climbing into the entry plug. The more she tried not to show her anxiety, the more obvious it became... to Rei, at least. That the Major was so concerned was a true testament to how much she cared for her 'children'.

Pilot Sohryu had more than enough confidence for everyone involved, and was more than willing to say so, repeatedly and seemingly as loud as was possible for her. Rei sometimes wondered if the German girl was more concerned with convincing other people of her perfection, or herself.

Pilot Ikari was the only one in which Rei had seen a notable change. Where he had once been hesitant and even fearful, he was now surprisingly aloof. Instead of physically running away, he had put his feelings aside and accepted that this was unavoidable. He was one of the few people with the ability to fight the Angels, and his leaving would only make things worse for humanity. Someone else could be chosen, but they would be less capable, and more likely to fail.

As if he sensed her attention, Ikari lifted his head and met her gaze. Rei was a little startled when his feelings returned briefly, and only then to grace her with a small smile. Even more surprising, she felt herself returning the gesture, despite the fact that she hadn't intended to. Ever since he had encouraged her to smile after defeating the fifth Angel, it had become somewhat easier to do so, but only with him. In truth, Rei didn't feel anyone else would appreciate her rare smile as much as he seemed to.

"We're ready for you," Dr. Akagi suddenly announced. "Pilots, proceed to your EVAs."

Pilot Sohryu immediately took the lead as she strode into the EVA cages, with Ikari following, and Rei herself bringing up the rear.

"Try not to keep us here too long, Third Child," Pilot Sohryu muttered over her shoulder. "I have plans tonight."

If Ikari heard the comment, he wisely chose to ignore it. Although, once Pilot Sohryu was out of earshot, he glanced over his shoulder as well. "Good luck, Ayanami."

There was a time when Rei would've disregarded such a comment as meaningless, and made no reply at all. Instead, she felt a certain desire to respond to Ikari's well-wishing, and did so. "I suspect you will also perform admirably, Ikari," she murmured.

"Thanks." He aimed another smile at her before approaching Unit 01.

Though very few people noticed it, Rei faltered for a step as she turned her attention to her own Unit 00. However, she quickly regained her composure and walked toward the EVA, staring into its single, imposing, orange eye. As she did so, there was only one thought running through her mind.

'I hope she isn't angry today...'

* * *

As usual, there were only two other people in the park. One was a tall, severe-looking man with a thick beard. He wore glasses that did an excellent job of hiding his eyes behind a white glare, so long as he kept his head perfectly aligned with the early afternoon sun. To this end, he was merely sitting on a wooden bench, not moving at all.

The other person was a small, blue-haired girl in a simple red dress. She was sitting in the center of a sandbox near the bench, carefully drawing what appeared to be an oversized cross with her fingers. Once done, she looked as if she were about to lay on it herself, but suddenly noticed that they were no longer alone. She raised her head, crimson eyes narrowing slightly as she finally took in the silent form of Rei Ayanami staring down at her expectantly.

"It is you again," the child murmured as she dusted the sand from her hands. "What do you want now?"

Rei chose her words carefully. "I am sure you already know that."

"I am busy," the girl replied coolly, indicating her sand drawing. "What do you want?"

"For us to coexist peacefully, for as long as there is a need."

There was no audible reply, but it was clear from the girl's expression that she was not at all fond of the idea.

Fortunately, Rei was prepared for that reaction. "As I recall, our individual feelings on the matter are irrelevant. You know that everything I do, I do to serve my purpose. His purpose, for me." She allowed her eyes to stray to the man beyond them, and was not at all surprised to find the child doing the same thing.

The girl seemed to change her mind after a moment. "Very well. Let us do this quickly." She glared intently up at Rei's face with all the dislike her tiny body could muster.

The sensation that followed shortly after struck Rei hard enough to make her stagger on her feet. Her legs finally gave out as blinding pain overwhelmed her mind and body, agony racing through everything she could still feel.

A minute later, the majority of the pain was gone, leaving only a throbbing headache in its passing.

It was clear that she was meant to remember this feeling of complete helplessness.

The girl made an odd, quiet noise. "You have been busy..."

"I told you," Rei whispered as she sat up. "I have a purpose. I must-"

"Who is this?" the girl asked abruptly.

Before Rei could reply, an image of Shinji was forced into her mind's eye. From the concerned look on his face, she recognized it as the first time they'd met in the EVA cages. "He is... a fellow Evangelion Pilot. He is Commander Ikari's son." Noticing the girl's blank stare, she quickly added, "Gendo's son."

"I do not believe you," the girl said calmly. "He does not have a son. He does not need one. He has me." The last word seemed to echo all around them, hanging in the air like a living thing for several seconds.

Rei shook her head slowly. "Why would I bother to lie? If you thought I was lying, we both know you could easily extract the truth."

The girl glanced over her shoulder before lowering her head. "But... I am his child," she muttered.

"You have nothing to fear. Gendo abandoned his son long ago. That is something Shinji seems reluctant to forget or forgive completely. They will never have the kind of relationship that you and Gendo do. Shinji is only here to fulfill his purpose, as well."

"What purpose?" the girl asked at once.

"To protect the people that are important to him."

"Like you?"

Rei did not miss the accusing tone in the girl's voice. "Perhaps."

"Why did you let him in?"

Before Rei could answer, she was fed an image of Shinji in his plug suit, sitting inside Unit 00's entry plug. "That was not my decision."

"I don't want him in here," the girl insisted. "I don't like him."

"It was a cross-synchronization test."

From the blank expression on the girl's face, the words meant nothing to her.

"In the event of an emergency, should it become necessary for Shinji to pilot another EVA-"

"I don't want him in here again," the girl interrupted firmly. "Don't let him in."

"You have more control over that than I do," Rei added.

"Explain," the girl demanded at once.

"Shinji would only be expected to pilot Unit 00 if I were completely incapable of doing so."

The girl stared at her for several seconds. "You mean I have to choose between either you, or him?"

"Correct."

"Don't let him in."

"If that is your desire, then I suggest you do not allow our arrangement to deteriorate to a point where that would become necessary."

The girl's red eyes closed. "It's hard. She comes out sometimes."

Rei blinked. "To whom are you referring?"

As if she knew any description would fall short, the girl merely opened her eyes. The right one was red, just as it had been seconds before. The left one was red as well, but it was spinning wildly in her head, and seemed to have nearly doubled in size.

"She can't help it," the girl whispered, her voice thick with pain. "She has nothing. She only knows to cling, to anything and everything. If I hadn't stopped her last time..."

"Shinji would still be here," Rei whispered.

"It wouldn't work well," the girl muttered, shaking her head. "Not as well as... us. I can't make her understand that it's better, this way."

"No one could. She is empty. She desires wholeness, even if she has no idea what that would mean."

"What do any of us know of wholeness, now?" the girl asked.

Rei paused, knowing what she would say next could cause problems. "We are at least two halves."

The girl glared up at her, one eye still spinning madly in her head. "I said I would put up with you, but that's as far as it goes."

Rei shook her head. "We will need more than that, if I am to remain the Pilot of Unit 00. You yourself admitted that was the best option for all of us."

"So what else do you want?" the girl snapped.

"I think," Rei said slowly, "that I will need to speak to her."

The girl paled slightly, her stance becoming much more passive. "She can hear you," she muttered softly.

Rei crawled forward and gently pressed her hand to the girl's left cheek. The spinning eye swung immediately towards her touch, and then to Rei's face, before wandering aimlessly again.

"I am sorry," Rei whispered. "I would end your pain, if I knew how. But if you will trust me, I-"

* * *

"Rei? REI!"

Rei's eyes snapped open at once. Major Katsuragi and Dr. Akagi were both leaning over her, worry written all over their faces. Just beyond them, Shinji had the same expression. It took her a moment to realize that they must have dragged her from the entry plug. She had taken too long this time, apparently.

"Was my synchronization ratio acceptable?" Rei asked.

They continued to stare at her, but after a moment, Dr. Akagi checked her readings. "Yes, a little better, in fact. Whatever you were doing keep it up."

"Unless it causes more incidents like this," Major Katsuragi added, shooting the doctor a dark look. Dr. Akagi just shrugged and moved away.

"Are you okay, Ayanami?" Shinji asked, leaning a little closer.

For a moment, Rei was tempted to glare at him, but quickly reminded herself of who he was, and more importantly, who she was. "I am fine, Shinji," she replied.

He looked completely startled, and so did Major Katsuragi.

"You've never called me that before," he murmured softly.

"No, I haven't," Rei agreed, and that was all she said.

Indeed, she had always called him "Pilot Ikari," at least out loud. But more recently, in her head, and within Unit 00, she had begun to think of him only as "Shinji." She understood there was a vast difference between the two, and clearly, so did he.

But only now did Rei consider the fact that "Pilot Ikari" could in fact refer to another person, and perhaps because she could still feel the effects of the synchronization test, the words left a bitter taste in her mouth. It didn't seem right to associate Shinji with that unpleasantness, despite his undeniable connection to it. Then again, Rei thought sadly, sometimes such connections were completely unavoidable.

**The End.**

* * *

Endnotes/Rant:

This will be LONG, you may want to skip it, but it does explain the story better.

I don't believe that even Gendo himself knew everything there was to know about Adam, Lilith, or the rest of the Angels. He probably had a better idea than nearly everyone else at NERV, but seeing the way Kaoru interacts with people, I can't wrap my mind around any pure human (in the sense that they don't have stolen Angel DNA, that is) being all that knowledgeable about the nature of Angels. Look at the way people react to Rei and Kaoru. NO ONE understands them. They make people confused, uncomfortable, and nervous. Gendo thought he understood Rei, and he was wrong in the end. Keep in mind that it was humans that "created" Rei and Kaoru (or at least gave them souls). To me, this says that even in the hands of men, Angels can't really be controlled, at least not for too long. I suspect they were never meant to be servants to humans, just that this assumption by humans was destined to cast both sides into war. Every Angel in human captivity broke free by the end of the series, in some form of another.

The popular "proof" of Naoko Akagi's soul being in Unit 00 is when it attacks Rei, and then supposedly Ritsuko. I agree that is proof that whatever is inside Unit 00, it clearly doesn't like them. But, let's assume that it is Naoko in there. How in the world could Rei have piloted an EVA containing the soul of someone who murdered her? Since the idea is for the soul in the EVA to be protective of the pilot (motherly, literally), this makes no sense. If anything, there should have been way more incidents of Unit 00 going nuts throughout the series, yet Rei seems to have no trouble at all with the EVA after a certain point.

Rei does later develop (or reveal, no telling how long she had them) Angelic powers. You could argue that she got them from Lilith's soul, or being partially merged with an Angel shortly before her second death. And maybe among these powers is Kaworu's ability to override the soul inside an EVA, as he does with Unit 02. If that is the case, perhaps this is why Rei can pilot Unit 00 with no further trouble. Though, if she did have that ability all along, why not use it earlier? If nothing else, it would've saved NERV some money in self-inflicted damages to Unit 00 (assuming Rei cares little about her own pain and suffering and more about Gendo's success).

Now I'll discuss my own position. When inside Unit 00, Shinji sees and hears nothing but visions of Rei. This ruined the idea of Naoko being in there for me. If the images were violent, or of Rei (or even Yui) being strangled, that would be one thing. They weren't. From that, three possibilities come to mind: 1) Unit 00 (having no complete soul of its own) is imprinting on the mind/soul that pilots it most often, 2) the partial soul inside Unit 00 is that of a former Rei, 3) something in the EVA triggered the visions in Shinji (maybe he didn't have visions in Unit 02 because he and Asuka aren't "related").

Wait, it's been pointed out that each Rei has had the same soul: Lilith's. So it shouldn't be possible for it to exist in two places at once. I'm not so sure. First, I seriously doubt that extracting and transferring human souls is a perfected science. Certainly doing the same to an Angel involves plenty of guesswork. So putting a human soul inside of an Angel-born EVA seems crazy and risky at best. And considering how many times the EVAs did things they supposedly "couldn't" or "shouldn't" have (particularly Unit 01, who comes from who? Lilith...), are we really expected to believe that these people knew exactly what they were messing with? Let us not forget that Lilith has a reputation for being defiant, especially where males (i.e. Gendo) are involved. And I really doubt Lilith is happy, being nailed to a cross while people (her own children, no less) hack off parts of her. So I don't think it's too much of a stretch to say that anything belonging to Lilith, no matter how much it's been manipulated by men, is eventually going to break free and develop its own will, or at least follow Lilith's.

What conclusions was I trying to make in this story? After careful consideration, I've decided that Rei I is not the soul in Unit 00. That is, she can't be, because her soul is technically in Rei II, the pilot. However, an overused comment about Rei is that she's an empty shell. But we know that a Rei body can exist without a soul, at least in the Reiquariam. Who is to say that a remnant or incomplete copy of Rei's (Lilith's) soul can't exist without a body? We know that EVAs are great for housing souls, in the sense that the souls never seem to completely leave Units 01 and 02. Perhaps the partial essence of a Rei remains in Unit 00 (either purposely put there, or somehow leaking in). For the sake of argument, I'll say it's Rei I, since she's the only Rei we know for sure had the soul before Rei II.

This brings up a good question: wouldn't the two Reis get along fine? Not necessarily. When faced with the idea that there is someone else who is almost exactly like them, most people feel pretty threatened that they'll be replaced, and this is a valid fear for Rei I and Rei II both, since they ARE killed and replaced. Most Rei clones would be alike in that they only had Gendo and his purpose as an anchor in their so-called lives. This is especially the case for Rei I, a child who would consider him a father, and be even clingier as a result. Children can be pretty irrational people when they get upset. With Rei II always climbing into Unit 00, Rei I wouldn't be all that welcoming, at first. In addition, conflicting and incomplete memories on both sides just complicate things. Rei I knew Gendo before NERV, Rei II knows him as Commander Ikari. Gendo and Unit 00 are all Rei I has left. Rei II has those, and Shinji. Shinji inspires feelings in Rei II that Gendo doesn't, feelings that Rei I couldn't have: she doesn't know Shinji. But despite their differences, both have a devotion to Gendo that outweighs just about everything else. Rei II even tells Asuka that she would take her own life if Gendo told her to, but when she finally does, it is to save Shinji. Some assume it's her motherly instinct kicking in, and I don't disagree. But I wonder, why did the Angel appear to Rei as herself? If it was trying to convince her to merge, and it could read her mind, wouldn't Gendo or Shinji have been more effective? Seeing herself didn't seem to bother Rei all that much. Almost like she was used to talking to someone who looked like her…

Rei also tells Asuka that her EVA has its own mind. I thought that was odd. Why not say soul instead of mind? I think Rei was making a distinction between the human soul and the EVA's mind, as if to say that an EVA can think for itself, independent of when the soul is in control. It's easy to assume that whenever an EVA does something on its own, it's the soul that does it. But maybe it's more that the soul communicates with the mind of the EVA. EVAs were "made in the image of man," yet they act more like beasts when the pilots aren't in control. To me this implies that the EVAs are more animal than man, but that they can react in the interest of the soul. Yui would no doubt lift her arm to save Shinji, but would she run around on all fours and eat a corpse? That's the EVA's true nature coming through, not Yui's, and if she were speaking to it, all she probably said was "protect Shinji and grab the S2 organ." The EVA's beastly mind translated that into eating the organ, as opposed to absorbing it through the hand or any other way (at least, the possessed Unit 03 didn't have to do it orally). Certainly the souls aren't ALWAYS in control. Would Yui kill Shinji's friend by crushing an entry plug already outside Unit 03? Once the entry plug is ejected, the EVA should deactivate. This isn't always the case, but the discarded entry plug is no threat, the pilot-less EVA is. If Yui were in control, it's far more likely that she would've tossed the entry plug away and focused on destroying the EVA. Why cause her son unnecessary pain? I assume that the EVA's mind had no problem with the dummy plug, and that it is Yui who rejects the dummy plug after that point, knowing that the EVA running under the Dummy Plug system might do further harm to Shinji's already fragile mind.

So that's what I think... or what I thought around the time I started this, which was March 2006.


End file.
